Cubase should not change the content without your permission, it should simply import the modified file as a new file in the pool even if it has the same name and path. I’m talking about the scenario where you have selected “Copy to project” when you drag and drop the file, so the old version of the file is already in the “Audio” folder. Cubase should simply realize that it has changed and copy this new version to the “Audio” folder (maybe with a “(2)” suffix to differentiate it from the first one).
This is very inefficient in my opinion. Ableton Live or Studio One handle perfectly what I’m describing here.